Upgrades
by Thunderchin
Summary: The Federation has been hard at work engineering some new weapons for their troopers, but the Marines field-testing them have lost contact. Samus is sent to find them and prevent the tech from falling into enemy hands.
1. Prologue and Chapter One: Mission

PROLOGUE:

Galaxy Federal Police, Unit M405  
Transmission Log Entry #  
Transmission Recipient: Samus Aran, Human Female Bounty Hunter

Transmission Contents:  
Eight days ago, we intercepted a distress signal from a squad of GF Marines near the planet SR-391 while they were combat-testing various prototype weapons systems (Details classified to Level 5 Clearance) on a known Space Pirate stronghold. We believe there are a minimum of casualties, but injuries and material damage have gotten the better of the squad.

It is known that the Space Pirates are too strong for conventional troopers, so it has been determined that a single lone bounty hunter inserted into the fray would better achieve our goals of extraction.

Contract Agreement: Locate and retrieve the survivors, if any. Also locate and either retrieve or destroy any Federation prototypes before they fall into enemy hands.

Coordinates: [Sol]280-010:10LY Planetary Sector AK-47

Good Hunting, Samus...

-  
CHAPTER ONE: Mission

A slight jerk accompanied the gunship exiting warp speed and decelerating to normal velocities.

So the old freighter saying was still true, Samus thought, not even the best inertial dampers can stop the jerk of entering or exiting warp.

WARP ENGINES OFFLINE - COOLDOWN COMMENCING

Samus switched the Gunship to its sublight drives and aimed the nose ahead to her destination. What loomed just in front of her (about 100,000 kilometers off the bow) was a mostly blue planet, with splotches of jade green and dusty brown. After double-checking the coordinates, she gunned the engines and set the autopilot. She had much more important things to do than sit there and pilot the ship.

She stood from the cockpit chair and walked out the back hatch, to a compartment in the interior of the Gunship. Here resided a small living quarter and her Suit diagnostic terminal. Tapping the screen on the terminal, she checked the progress on suit repairs.

CHOZO VARIA SUIT - SUIT REPAIR UNDERWAY  
PROGRESS - 40%  
ETC (Estimated Time to Completion): 4 HOURS

Perplexed, she reentered the cockpit to check on the flight. By habit, she checked her viewport first, but just as she saw what she saw, the instruments squawked to life.

PROXIMITY ALERT. PROXIMITY ALERT. COLLISION WARNING.

Samus cut the engines and fired a quick burn from the retro-rockets as the wreckage from what appeared to be a Federation vessel lingered in the view.

SCANNER DATA: Federation Squad Carrier _Inferno_: This is the ship of the Galactic Federation Marine Corps, Squad No. 7. This squad has been provided with several classified prototype weapons systems, and have been involved in combat testing. This squad is currently MIA and presumed mostly alive. Last Known Location: Planet SR-391. Scans of the ship indicate the lifeboat has been launched successfully. No bodies, dead or alive, detected within or in vicinity. Lifeboat absence leaves room for the Gunship to dock.

Samus punched the code into the Gunship computer, and it replied, DOCKING SEQUENCE COMMENCING. STANDBY FOR AIRLOCK OPENING. Then she walked to the terminal and decided that it couldn't hurt to don the partial suit, just for five minutes.

The suit pieces materialized in flashes of light, orbiting her body as they integrated into the pieces of the suit. Slowly but surely they slid onto her body as more pieces materialized, getting larger as the process continued. Soon the underlayer was nearly completely assembled, and the larger over layer plating attached over. The layers then, in a very intricate pattern, linked together, tightening around Samus' tall, slender frame. The half-tube that was her arm cannon floated up to her arm, and the other half of the tube closed and locked around the arm. In no time the suit was completely assembled from the neck down.

"Time for the final piece," said Samus to herself as the helmet sides formed around her ears and snapped together around the back. The top of the helmet locked into place above the sides, bringing with it the Oxygen Supply Equipment which formed a mouthpiece and the front of the helmet. Finally, the Visor, being hinged about the sides of the head, flipped down into combat position, forming an airtight seal.

"Let's rock." mumbled Samus as she boarded the lift to the airlock.


	2. Chapter 2: Clue

CHAPTER TWO: Clue

With a slight hiss the airlock opened, and up went the lift that transported Samus out the topside hatch. There she stood, for about a second, atop her gunship, and then she leaped down with a flip, sticking the landing perfectly. As she recovered, her suit finished rebooting, and now a message flashed across the Visor: SUIT REPAIR INCOMPLETE. MISSILES OFFLINE. BOMBS OFFLINE. GRAPPLE OFFLINE. SPACE JUMP OFFLINE. GRAVITY SUIT OFFLINE. WAVE/ICE/PLASMA BEAMS OFFLINE. ALL OTHER SYSTEMS OPERATING AT FULL CAPACITY.

Samus, thinking she was only going to need this for five minutes or so, decided to move on and let the ship repair her left-behind suit parts. She walked to the airlock door that had once sealed to a lifeboat. Now, with hull breeches flagrant aboard ship, no air remained, and thus the door was unnecessary. She tapped the panel, and the door slid open partway. Using some elbow grease, Samus was able to get the door opening wide enough for her to pass into the crew cabin. Here, the hull had been pierced right through, with large corresponding holes to prove it. Sparks of electricity showered from the roof. Displays flickered error messages everywhere.

Samus strode slowly through the main aisle between the rows of seats, making her way to the bridge. There was no apparent cause to all this mayhem and destruction, and worse, no signs the Troopers had even been there in the first place. No blood, no bodies...it didn't make sense.

There's gotta be a way to explain, Samus thought to herself, there's gotta...

At this point she had entered the bridge, where the computer equipment was all just like the stuff before: broken, battered, bruised. But as she turned away a console in particular caught her attention. She whipped back around, and in her investigation found the non-flickering display in front of the Captain's chair, with a keypad being displayed.

SCAN VISOR DATA: GFS _Inferno_ Ship's and Captain's Logs successfully downloaded for further review.

Then...

SCAN VISOR DATA: Unauthorized access to computer system detected. Critical Damage detected. Autodestruct activated. Countdown started at 00:30:00.

The remaining ambient lights flashed red, indicating the countdown had already commenced. Samus sprinted back down the aisle, through the airlock, and jumped to the ship effortlessly. As she was doing so, she had already punched in the remote commands to the ship to take off. Sure enough, it did, just as Samus was being lowered back into her ship, and gunned the engines for a quick getaway as the blast consumed the ruins of the _Inferno_.

As Samus' Gunship fled the scene towards SR-391 itself, it was, at the moment, unaware of any other danger. Unaware it may have been, but danger hadn't left yet. It simply had to be uncloaked.

"Samus' ship has escaped the trap we set, sir," stated a Space Pirate on the scanners of the ship _Sparrow_, orbiting SR-391.  
"Good. Keep tracking it," responded the Captain in a deep voice, "right where we want her to be." 


	3. Chapter 3: Meeting

CHAPTER THREE: Meeting

PLANETARY SCANNERS - WRECKAGE DETECTED. ORIGIN OF CRASH - GALACTIC FEDERATION  
Suitable landing site located one half kilometer from crash site.  
Beginning landing procedures...

EQUIPMENT REPAIR COMPLETE - MISSILE LAUNCHER ONLINE  
Capacity restored for 30 Missiles.

The Gunship floated gently down to the rich, vegetation-laden surface below. This particular landing site was actually a small sinkhole in the surface of the planet, about three hundred feet deep and with a radius about the length of the Gunship itself, that featured an appropriately-sized waterfall and a deceptively small pool of water below. The walls were smooth, but with deep grooves in them, big enough to serve as tunnels even for the biggest of men. And, as Samus noticed as she rode the lift out the hatch, it looked like someone had been here before, as metal doors within human-sized tunnels did NOT just grow from random vegetation. She hopped off the Gunship's roof and headed to the lowest part of the grooves. One jump got her up into the grooves themselves, and she followed them up in a spiral towards the top. She passed two doors on the way; one with a green lock on it, the other with a blue one.

At the top, there stood a door with a white center, which one blast from the Power Beam promptly opened. A subterranean corridor led from this white door to another a short distance away, which Samus also blasted and went through.

And found herself in the shadow of a ten foot rise, in the flat of which lay the door she had just gone through, in what looked like expansive rolling hills and grassy meadows. To her right (as she came in) ran a stream; this looked like the boundary between the hills and the slight depression in the ground she currently stood. To her left rose a wall of stone about fifteen feet high. The regular construction of the walls, and the regular placement of parapets along its top hinted even further of strange things. Along the surface facing Samus, were deep blackened pockmarks, signs of a battle.

The river side would be the perfect place to stage an attack, Samus thought, placing herself in the aggressors' shoes. She turned back to the right, hoping to find corpses from the attack on the mysterious rampart. In the tall grass on the other side of the stream, sure enough, were several Space Pirate bodies.

SCAN VISOR DATA: Space Pirate Commander Balrog, final entry. The infidels from the Galactic Federation have done it again! We attack, and they bring out weapons never before even conceived. High Command tells us these are but mere prototypes, and that we but lab rats to their scheme. How many troops do we have to lose to these infernal creations before we are capable of capturing them ourselves?

So the squad survived, thought Samus. She had already figured as much by the underground tunneling that had just linked this area to her landing site. She had also figured the Federation Marines were able to construct more sound defenses like the stone rampart behind her, all around where they had set up base.

Since the last boundary had no door in it, she retreated to the hole in which she had parked her ship, exiting out the blue door using a Missile.

Another short subterranean tunnel led to...another rolling hills meadow, with a stone wall all around the left (as she entered) for about a quarter kilometer, before hooking to the right and back down the right side, ending at a hill. Again, parapets lined the top edge of the barrier, but this time ladders had been prepared against the walls, apparently in case the people defending it needed to get in or out.

But smack in the center of this area was a fragment of what looked like a spaceship. From analysis, neither Samus nor the Scan Visor could identify it.

SCAN VISOR DATA: The wreckage is damaged beyond recognition. A barely intelligible Galactic Federation symbol adorns the top side.

She had just started to recover when suddenly, out of nowhere, several armored men emerged from cover. A quick count revealed some missing; these men who were present were probably the survivors. As Samus looked around, several armorsuits had had so much damage as to be missing entire plates and/or have deep gashes in the plating.

"Ah-ha-ha." Samus knew that laugh instantly. It came from behind, and as she quickly snapped around to face the source, a man with armor and a red helmet removed the helmet. "I see the Fed cares about us after all..."


	4. Chapter 4: Update

CHAPTER FOUR: Update

"I hope the Fed cares about us, and not just because of our hardware. Though if I were the inventor, I know I'd want it back, too," the mystery soldier continued, before realizing his mistake of not introducing himself. "I am Lieutenant Link."

The removal of the helmet had revealed a boyish face with blue eyes, sandy blonde hair that ran in spiky locks, pale skin, and slightly pointed ears. It was almost a shock to see this face on a man who had an inch on Samus' 6'3". He extended his hand for a handshake. "It's an honor to meet you, Samus."

Samus, surprised, flipped over her left arm and obligingly shook Link's hand. "It's a pleasure meeting you, Lieutenant. Where is your captain? I'm sure that this isn't all the survivors, right?"

Link chuckled. "No, it's not. We're just a party moving to secure the last missing pieces of our escape craft before the Space Pirates find them. Not to mention we're looking for supplies scattered about during the collision."

Samus took a moment in her head to praise the good decisions on the part of the stranded. "No wonder you've lived eight days like this. You all deserve commendations, the whole lot of you."

"We're just doing as we've been trained, ma'am."

Another trooper, whose gear Samus had never seen the likes of, interjected, "Sir! Base Camp is reporting bad, bad news! Space Pirates have discovered them again! They got cavalry all over them, and they're no match for this stampede!"

And yet another trooper piped up three seconds later, "Sir! Enemy transport inbound!"

Link snapped his helmet back on, barking, "Move to cover! Lay down fire on the baddies as they drop! Don't let them hit the ground!" Then to Samus, "Please take that thing out of the air."

The troopers moved to comply, as best as they could amid the hail of cannon fire the skiff's dual under turrets placed in the area. Their machine guns, trained on the underbelly where the cannons were, burst to life, but in vain. The bullets simply ricocheted off the armor plating.

The guns would not let up, and the Federation Troopers were pinned. Samus managed to draw partial fire, but her Missiles weren't working either.

And the doors on the skiff opened, revealing twenty Space Pirate soldiers. On just the ten Federation combatants, the Fed didn't stand a chance. But with Samus there, it was already a whole new ballgame.

Not to mention the Federation had a secret arsenal...


	5. Chapter 5: Consipracy

CHAPTER FIVE: Conspiracy

"The ground forces have engaged the Federation scum, Lord Ridley," said the Captain, in front of the viewscreen.

"Is Samus there?" asked Ridley.

"Yes, she is. She's with the Federation now."

"Does she know of anything besides ground?"

"There is no reason to conclude she knows about our little trap."

Ridley pondered this for a moment, then said, "Keep her alive if you can. If you must kill her, then you must kill her. But I would like to have her alive." Another pause. "Oh, and one more thing..."

"What is it that you wish to ask, Lord?"

"They were using the base as a testing ground for prototype weapons systems, right?"

"They sure were, Lord."

"Then take their weapons, and have your Science Team figure them out. They will pay off in the end..."

"Science Team is already working on that."

"Captain, you have done well. You shall certainly be rewarded for your accomplishments. We'll be seeing you later, Captain."

"Thank you, Lord. Sparrow out."

Several Space Pirate researchers, deep in the bowels of the ground installation, were compiling observations and recorded effects of the weapons being used against the forces. Their research was slick, efficient, and extremely effective. The final report sent to the Captain read:

Science Team reporting to Command. We have found a theoretical conclusion as to strategies involving enemy possession of superior firepower, and replication of it. Actual samples of the weapons are needed for conclusive testing and structural analysis, but observations taken from combat footage shows quite a bit of information surrounding the enemy's new arsenal. We are sure that, with more time, money, and resources, that replication of these features is an investment that could pay dividends for our cause.

Ridley, fresh from his private communique with the Captain, turned to the Space Pirate ensigns running his personal command ship and ordered, "Set course for maximum warp jump. Destination: SR-391."


	6. Chapter 6: Defense

CHAPTER SIX: Defense

In the shadows of thick forest crouched several Space Pirate recon scouts. They each had a Scanner in their left claws, and were taking readings and bearings.

Said the recon squad leader, "I think we found them."

Replied one inferior, "At long last, we shall purge them from our territory."

The survivors were bracing themselves for another day behind enemy lines when the man on watch sounded the alarm. He then reached for his radio and screamed into the mic, "Captain, the Space Pirates found us. They're bringing the whole kit and caboodle."

Captain Roberts, the leader of the surviving troops, immediately responded, "Where are they coming from? I'm mobilizing the forces now."

"From the east, sir."

Several moments later, all the survivors who had stayed at the crash site were pouring out of their shelters and arming themselves. Roberts and his underlings were barking orders through this melee, as ammo boxes and belts were passed around. Soon after that, the Space Pirate forces were in close enough range for the squad's two heavy gunners to open up with their .50 caliber machine guns, taking out the first rank.

The second rank put up their personal energy shields, blocking further gunfire. This was where the second line of defense came in. A series of landmines detonated, and the second and third ranks were obliterated.

But there were dozens more ranks of troops, and several tanks too. Not to mention aerial support was certain. The Federation Troopers opened up with their rifles, and the Space Pirates did the same. It was now a fight to the last, and the Federation was outnumbered.

"Piper, take out that tank with your heavy cannon!" screamed Roberts at his mobile artillery specialist, referring to the experimental Plasma LANCE that adorned the right shoulderpad of Piper's bulkier-than-usual armor.

"Got it!" Piper replied, firing a burst of three plasma shots at the lead Space Pirate tank. The shots hit in the cockpit, the left hover pad, and the gun turret in that order, and the tank exploded, its burning shell making a sharp THUD against the ground.

And as more Troopers fell on both sides, Roberts went to the ammunition locker. Given the long wait for extraction, he was not surprised to find the rifle ammunition was gone. Oh well, he thought as he picked up an ammunition box marked ".45 ACP 100 ROUNDS" and frantically started loading the magazines for his sidearm, the ancient but still useful Model 1911 pistol.

Elsewhere in the melee, the Space Pirates had managed to get within striking range, and this was where they excelled. Their Wrist Bayonets, standard issue to every trooper, clearly overpowered the lack of melee weapons of the Federation.

But there was another experimental weapon, an adaptation of a club used by ancient humans to wage war. The three troopers in that area of the fight not mowed down by the Wrist Bayonets took out what appeared to be short sticks, that were fat at the end and skinny at the grip. The Space Pirates stopped for a second to laugh at them, but then the first one found himself flying through the air. He had been struck with these sticks, which were actually loaded with Kinetic Energy Projectors that lent a great deal of force to the blow. The other two Space Pirates in that group advanced, and they, too, found themselves flying like line drives at the World Series.

But weapons were running out of ammunition. Men were dying left and right, to the point of only ten remaining. The Space Pirates were leaping all over the place, clearly outmatching the Federation. There were nine runners from that battle. Nine survived, and they ran to the west, and into a heavy wood in an effort to conceal themselves.

As for the tenth, Captain Roberts was still slaying Pirates left and right to cover the escape of his remaining men. Through the fire and flames, he bid his men goodbye, placing 45 caliber holes in Space Pirate brains before he, too, submitted to a hail of plasma fire.

The crash site was razed that afternoon, with supplies and technical documents being scavenged from the flaming, battle-damaged compound made from the remains of a crash. And as Space Pirates occupied that land, they radioed back to Command.

"My Lord, we have taken the infidels. Only nine remain, and they shall be hunted down to the last."

"Good," said the Captain on the other end. "Ridley will be pleased to hear of this. You have done well. Camp out there, and get some R&R."

"As you wish, my Lord."


	7. Chapter 7: Unity

CHAPTER SEVEN: Unity

Commander Link, his men, and Samus were outgunned in the field. And all that was facing them was the lone skiff!

"Let's get out of here!" suggested Link over the noise.

"Good idea!" Samus replied. "I'll cover you! You get your men to that door!"

"Gotcha!" Link gestured to his men as Samus moved to the other side of the skiff. Concentrating her fire, Samus managed to Missile one of those turrets to pieces.

But the other one was the problem. The turret had eaten all 30 of her Missiles, leaving her with a Beam weapon as her only defense. She searched frantically for a solution to this problem of running out of firepower, and found it immediately.

She was staring right at the engines.

It was at that moment that one of the other Troopers, seeing the exact thing, decided to use his weapon. To Samus' surprise, three small hovering machines launched themselves from that Trooper's backpack. As the Trooper guided them, the drones ascended to the height of the skiff, and fired energy blasts at the engines. The small, precise shooting sheared off the drive fins, and soon the skiff's main engine turned out to be its own demise as the unregulated exhaust melted the rear of the craft. Without a drive, the skiff lost power, and came to the ground with an immense dust cloud and a deafening SLAM!

As soon as the drones returned to their dock, all the troopers and Samus exited through the door that Samus had entered through, taking them back to Samus' landing site.

While the rest of the Troopers waited, Samus docked with her ship, refilling her Missiles and gaining another repaired powerup.

EQUIPMENT REPAIR COMPLETE - BOMBS ONLINE  
Missile Capacity Increased to 40.

Samus returned to the troopers, who were in the process of unlocking the green hatch. Link explained, "This ought to take us back to the crash site. If they ran into trouble during our absence, they'll need our help if they want to live. This passage comes out at the other end in a hidden hatch. We should be able to surprise the attackers from there."

The green lock disengaged, and the door opened. Everyone made a dash through the adjacent hallway, and sure enough there was a ceiling hatch 800 meters down. Samus was the first to climb through the hatch and the loose brush that covered it, and the sight that awaited her shocked her to the very core.

"Are you sure this is the crash site? All I'm seeing are Space Pirates and a mangled, burning wreck."


	8. Chapter 8: Revelation

CHAPTER EIGHT: Revelation

Commander Link follwed Samus out of the hatch, hauling himself up to the ground above. He joined Samus, who was crouching behind a low bush for cover.

"This is bad," he remarked, hearing Samus' earlier statement. "That was our entire ammo supply. And I see we have a few casualties." He indicated several scattered bodies, all sheathed in Federation Power Armor. There were dozens upon dozens more of the Space Pirate variety, but it seemed there were enough Space Pirates living to make up for their dead.

Samus continued to study her enemy's movements. She and Link were on a small ledge with bushes for cover, overlooking a moderately sized clearing. Over on the opposite side and slightly to the left, the wrecked ship, aflame from the earlier battle, remained standing in its ruined condition.

Link pointed to three Space Pirate tanks near the center, their gun turrets patrolling the surrounding area. "If you can at least distract them, we can hit the infantry Pirates with no problem. Shouldn't take more than five minutes to clear them out if you help us."

"That's what I'm here for," replied Samus, preparing to leap out to begin her part of the fight.

Link turned to the other troopers, all seven of them who waited in the corridor below. "Alright, men. We're the only ones left, and we're about to come across some Space Pirates!" He gave several tactical orders after that...but Samus couldn't pay attention.

She was too busy somersaulting over the bushes into the clearing. As she did so, she charged up her Beam and took bearing at the first of three tanks. The Space Pirates saw her immediately, and various alarms sounded as they mobilized. They were firing as Samus hit the ground. But it was too late for the first tank, for as Samus hit the ground she had already aimed at it with a full charge. The blast struck the tank's turret, damaging it severely and knocking its aim off.

Several dozen Space Pirates were ganging up on her at top speed as she did this, but the sound of Federation rifles penetrated the sky, and they all fell from said rifles. The Federation troops were providing cover fire, spreading out and taking out the footsoldiers as Samus locked onto her damaged target and let off a Missile. The tank promptly exploded, and Samus backflipped out of the way of the shrapnel.

She moved onto the second tank, as the remaining two began moving around. The Federation troopers, all eight of them, had leapt down from their perch, engaging the Pirates in one-on-one. The aerial drones that one of them had were also doing alright, taking out enemies where neither Samus nor troopers could be. All Samus had to do was lather, rinse, repeat. It was easy to her...too easy, Samus thought. Oh well, at least further casualties could be avoided. Many a Space Pirate fell at the hands of her Arm Cannon, and the second tank was obliterated in short order.

"THEY'RE RETREATING!" Link called out over the radio, followed shortly by, "Wait...shit! They're getting away!"

Samus looked at the third tank...and saw that it and a cadre of Space Pirates were taking an early exit. She also saw something much more important, that some of the Space Pirates were carrying Federation equipment.


End file.
